Can now build a Docker image and run test suite including MQ, run as real user, DRMAA, CLI torque stuff, etc....

Allows run as real user stuff to work in an unmodified Pulsar root if these values are specified.

Will let travis ci see if this works.

Various fixes, doc updates, etc... as well as allowing dependency_resolvers_config_file and job_metrics_config_file to point at YAML files.

https://bitbucket.org/galaxy/galaxy-central/commits/5fac4d4b7d7d6b056056bf2a6094c7777dc28a71.

Can specify a dictionary of managers of the form:

managers:
  name:
    type: queued_drmaa  # defaults to queued_python
    option1: value1
    option2: value2

or just a single default manager with

manager:
  type: queued_drmaa
  option1: value1
  option2: value2

Breaking configuration and building stages out adds some consistency for how the default manager is constructed and will allow configuring managers via other mechanisms then the job_managers.ini file more easily (namely app.yml).

Configuration Overhaul (Part 1)

This is for values such as staging_directory, persistence_directory, etc.... Anything from app:main except for paste.app_factory.

Can specify the location in server.ini as app_config, otherwise is there is a file called app.yml deployed next to server.ini (or whatever .ini) this will be used.

The documentation state that this could be unset to disable persistence - this is not the case. Added a new way to do this (by setting it to __none__) and updated documentation in sample file. Also commented it out in the sample file.

...regardless is being loaded from the command line or from a WSGI server.

Just use the same default throughout the app.

Reduces duplication and places more logic where it can be tested more easily.

If something went wrong before during pull down results from Galaxy - it would just take the error json as the input file. Likewise - it would not fail jobs if the postprocessing failed to publish - leaving empty green files in the Galaxy history.

Uses Kombu style retry parameters since we are already exposing those for message publish retrying. See job_managers.ini.sample for specific new options.

Lots left to do - integration test of this and retry framework for client side actions.

Improve publish logging.

Assign each publish message a UUID and include this in error handling.

Pull in Nate's updates from Galaxy and add some WIP I gave on quickly.

Log some more problematic conditions. We had removed logging during publish message but that was because we were logging whole message - hopefully this level is more appropriate.

acknowledging setup messages and failing when it was really just busy
staging large files.

Fix several typos in the docs

Poster is not the best candidate because it is kind of old and likely uncompatible with Python 3 - but is available in Galaxy. Should be targetting requests + requests_toolbelt I guess.

Add integration test for Slurm CLI job interface, add a bunch of unit tests for all CLI job interfaces. Correct small bugs discovered testing. More use constants and improved error handling.

Fixes failing TravisCI integration test locally.